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Six children were killed after a train collided with a school bus near the village of Mafube outside Middelburg on Wednesday.
Nineteen pupils were injured in the crash.
The death toll for the accident was revised up to six on Thursday morning from an initial five.
"The sixth learner succumbed to injuries while receiving treatment at the nearby hospital," the provincial transport department said in a statement.
The crash happened when the school bus, which was transporting about 30 students, crossed a railway line as the train was approaching, the department said.
"We cannot lose such young and innocent lives due to recklessness," the government said, adding that "people need to take accountability for their negligence."
The bus driver and train driver were also recovering in hospital, the provincial ministry told AFP.
